The rice-based agriculture of the Indian subcontinent has been interwoven in the rich socio-cultural fabric of the country. Of which, bio-culturally diverse North-Eastern states nurture thousands of landraces with poorly tapped agronomic traits. In the present study, 27 standard microsatellite data from 171 rice landraces from six states were analysed to understand their genetic diversity and population structure. Further, combining with a global dataset, we determined subpopulation identity using both model-based and multivariate analyses to uncover their history. We found moderate to high genetic diversity and high differentiation [standardized G”ST = 0.57]. The AMOVA partitioned overall variance into within population (75%) and among population (25%). The landraces from six states remained at various degrees of differentiation (pairwise FST = 0.09–0.41). We have detected a preponderance of aus-type in a majority of aromatic landraces. Rests were japonica and admixed with a little representation of indica. The presence of aromatic aus probably implied assimilation into local culture from the primary aus growing region of Bangladesh and India. Likewise, the arrival of japonica may stem from the exchange of goods among neighbouring dynasties via Southern and Southwestern Silk routes. The shared ancestry may reflect a merger of two ancient cultures. Our analyses also uncovered the existence of aus-type short and medium grain aromatic rice predicting an origin of aroma in aus subpopulation. Collectively, it demonstrated the diversity and divergent history of the rice landraces have been shaped by various socio-cultural interactions operative over time and space.

Rice landraces have been developed through artificial selection imposed by farmers during the long-term domestication process. Although the global rice diversity is well characterized, few studies have conducted an in-depth analysis of genetic diversity on a local scale. In India, there are many locally adapted non-Basmati aromatic rice landraces in which the pace of improvement is slow, despite their high economic values. The aromatic and quality rice landraces of Manipur, locally called Chakhao (delicious), are important, considering their high economic and cultural values. To conserve and encourage improvement of these landraces, we collected Chakhao accessions from eight districts of Manipur. The aim of the current study was to investigate the level of genetic diversity and structure of 37 Chakhao landraces based on genotyping with 47 microsatellite markers. The genetic diversity analysis revealed high gene diversity (0.673) within the Chakhao population, with values ranging from 0.303 (Poireiton) to 0.471 (mixed Chakhao). The Chakhao rice accessions could be divided into six subgroups based on genetic structure analyses. The population structure derived from the STRUCTURE analysis largely correlated with the farmers' classification of Chakhao landraces. The results of genetic diversity analyses and the indigenous knowledge of the names and use of Chakhao landraces would facilitate the conservation and utilization of this unique genetic resource.